The evolution of eyes.

Those of you who have been following this blog will know about the special issue of Evolution: Education and Outreach on the evolution of eyes that I edited last year (see below). There is now another excellent collection of papers on this subject in Philosophical Transactions of the Royal Society B, edited by eye experts Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin.



The evolution of phototransduction and eyes

edited by Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin
Philosophical Transactions of the Royal Society B, vol. 364, issue 1531, Oct. 19, 2009

The evolution of phototransduction and eyes
Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin

Evolution of phototaxis
Gáspár Jékely

The ‘division of labour’ model of eye evolution

Detlev Arendt, Harald Hausen, and Günter Purschke

Eye evolution: common use and independent recruitment of genetic components
Pavel Vopalensky and Zbynek Kozmik

The evolution of eyes and visually guided behaviour

Dan-Eric Nilsson

The evolution of irradiance detection: melanopsin and the non-visual opsins
Stuart N. Peirson, Stephanie Halford, and Russell G. Foster

Evolution of vertebrate rod and cone phototransduction genes

Dan Larhammar, Karin Nordström, and Tomas A. Larsson

Evolution of opsins and phototransduction
Yoshinori Shichida and Take Matsuyama

Evolution and the origin of the visual retinoid cycle in vertebrates
Takehiro G. Kusakabe, Noriko Takimoto, Minghao Jin, and Motoyuki Tsuda

Evolution of vertebrate retinal photoreception

Trevor D. Lamb

The evolution of early vertebrate photoreceptors

Shaun P. Collin, Wayne L. Davies, Nathan S. Hart, and David M. Hunt

Evolution and spectral tuning of visual pigments in birds and mammals
David M. Hunt, Livia S. Carvalho, Jill A. Cowing, and Wayne L. Davies

Evolution of colour vision in mammals

Gerald H. Jacobs

The evolution of eyes
edited by T. Ryan Gregory
Evolution: Education and Outreach, vol. 1, issue 4, Oct. 2008

Editorial

351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)

352-354. Introduction by T. Ryan Gregory (PDF)

355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)

Original science / evolution reviews

358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)

390-402. Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)

403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)

415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)

427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)

439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)

448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)

463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)

476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)

487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)

493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)

Curriculum articles

498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)

505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)

509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)

Book reviews

548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)

Evolution: Education and Outreach vol. 2 iss. 3.

The most recent issue of Evolution: Education and Outreach (vol. 2, issue 3) is now available online. I decided to sit this one out after six consecutive contributions (links below), but I will be back in the next issue with a follow-up to my previous article on selection.

Evolution: Education and Outreach
Volume 2, Issue 3
Editorial
Greg Eldredge and Niles Eldredge

Why I Teach Evolution
Greg Eldredge

Evolution in Biology Education: Sparking Imaginations and Supporting Learning
Kristin P. Jenkins

Evolution Education in Utah: A State Office of Education–University Partnership Focuses on Why Evolution Matters
Jerald B. Johnson, Marta Adair, Byron J. Adams, Daniel J. Fairbanks, Velma Itamura, Duane E. Jeffery, Duane Merrell, Scott M. Ritter and Richard R. Tolman

Why Science Standards are Important to a Strong Science Curriculum and How States Measure Up
Louise S. Mead and Anton Mates

The Growing Visibility of Creationism in Northern Ireland: Are New Science Teachers Equipped to Deal with the Issues?
Conor McCrory and Colette Murphy

Attitudes of Students at a Private Christian Liberal Arts University Toward the Teaching of Evolution
Troy A. Ladine

Addressing Undergraduate Student Misconceptions about Natural Selection with an Interactive Simulated Laboratory
Joel K. Abraham, Eli Meir, Judy Perry, Jon C. Herron, Susan Maruca and Derek Stal

Phylogenetic Analysis: How Old are the Parts of Your Body?
Robert K. Kuzoff, Seth B. Kemmeter, Jeffrey S. McKinnon and Courtney P. Thompson

Using Avida-ED for Teaching and Learning About Evolution in Undergraduate Introductory Biology Courses
Elena Bray Speth, Tammy M. Long, Robert T. Pennock and Diane Ebert-May

Using Inquiry and Tree-Thinking to “March Through the Animal Phyla”: Teaching Introductory Comparative Biology in an Evolutionary Context
James J. Smith and Kendra Spence Cheruvelil

“Evolution for Everyone”: A Course that Expands Evolutionary Theory Beyond the Biological Sciences
Daniel Tumminelli O’Brien, David Sloan Wilson and Patricia H. Hawley

Teaching Evolution Concepts to Early Elementary School Students
Louis Nadelson, Rex Culp, Suzan Bunn, Ryan Burkhart, Robert Shetlar, Kellen Nixon and James Waldron

Overcoming the Effect of the Socio-cultural Context: Impact of Teaching Evolution in Tunisia
Saïda Aroua, Maryline Coquide and Salem Abbes

Teaching Evolution with Historical Narratives

Esther M. van Dijk and Ulrich Kattmann

Preservice Teacher Understanding and Vision of how to Teach Biological Evolution
Louis S. Nadelson

Still More “Fancy” and “Myth” than “Fact” in Students’ Conceptions of Evolution

Deborah L. Cunningham and Daniel J. Wescott

Evolution in Lego®: A Physical Simulation of Adaptation by Natural Selection

Jakob Christensen-Dalsgaard and Morten Kanneworff

Does the Segregation of Evolution in Biology Textbooks and Introductory Courses Reinforce Students’ Faulty Mental Models of Biology and Evolution?

Ross H. Nehm, Therese M. Poole, Mark E. Lyford, Sally G. Hoskins, Laura Carruth, Brent E. Ewers and Patricia J. S. Colberg

From Newsroom to Classroom
Anastasia Thanukos

Science Standards Evolve
Eugenie C. Scott

Paleontology and Evolution in the News
Sidney Horenstein

Blogging Evolution

Adam M. Goldstein

Darwin: Origin and Evolution of an Exhibition
Chiara Ceci

In the Wake of Charles Darwin and Beyond: A Tribute to Ernst Mayr
Review of J. Haffer: Ornithology, Evolution, and Philosophy. The Life and Science of Ernst Mayr 1904–2005. Springer-Verlag, Berlin Heidelberg, 2007, 464 pp, $ 119, 00
U. Kutschera

A Permian Murder Mystery
Review of Extinction: How Life on Earth Nearly Ended 250 Million Years Ago, by Douglas H. Erwin. Princeton, Princeton University Press, 2006. pp. vii + 296. S/b $22.95
Matthew Williams

How Charles Darwin’s Early Years Led Him to Revolutionize Biological Thought
Review of The Young Charles Darwin by Keith Thomson. New Haven & London: Yale University Press, 2009, Pp. xii + 276, $28.00
Joel S. Schwartz

The Comparative Biology of Cultural Inheritance
Review of The Question of Animal Culture, Edited by Kevin N. Laland and Bennett G. Galef. Cambridge, MA: Harvard University Press, 2009. Pp. vii + 351. H/b $45.70
Lauren W. McCall

Nitrogen and the Carrying Capacity of the Earth
Review of Enriching the Earth: Fritz Haber, Carl Bosch, and the Transformation of World Food, by Valclav Smil. Cambridge, Mass.: MIT Press, 2001
Joseph L. Fail

My earlier articles:

Evolver Zone.

Readers of this blog will soon notice some changes. This is because the Evolver Zone site has now been launched, and Genomicron will be fit within it. For now, it will remain a separate blog at this same location, but the look will be updated shortly. Meanwhile, have a look at the resource of multimedia and information about software, databases, journals, and web links at Evolver Zone (www.evolverzone.com).

More on "evolution-proof" malaria control.

There is a second article set to appear on “evolution-proof” malaria control. I think this whole approach is important, but I certainly don’t consider it “evolution-proof” and I wish the authors didn’t insist on suggesting otherwise. Here’s the thing, folks: Plasmodium would be under selection if you mess around with their vectors. They can evolve, also.

Koella, J.C., Lynch, P.A. , Thomas, M.B., Read, A.F. (2009). Towards evolution-proof malaria control with insecticides. Evolutionary Applications, in press.

As many strategies to control malaria use insecticides against adult mosquitoes, control is undermined by the continual evolution of resistant mosquitoes. Here we suggest that using alternative insecticides, or conventional insecticides in alternative ways might enable effective control, but delay considerably or prevent the evolution of resistance. Our reasoning relies on an epidemiological and an evolutionary principle: (i) the epidemiology of malaria is strongly influenced by the life-span of mosquitoes, as most infected mosquitoes die before the malaria parasite has completed its development; and (ii) evolutionary pressure is strongest in young individuals, for selection on individuals that have completed most of their reproduction has little evolutionary effect. It follows from these principles, first, that insecticides that kill mosquitoes several days after exposure can delay considerably the evolution of resistance and, second, that the evolution of resistance against larvicides can actually benefit control, if it is associated with shorter life-span or reduced biting in adults. If a late-acting insecticide and a larvicide are combined, the evolution of resistance against larvicides can in some circumstances prevent the evolution of resistance against the more effective, late-acting insecticide, leading to sustainable, effective control. We discuss several potential options to create such insecticides, focussing on biopesticides.

Read, A.F., Lynch, P.A., Thomas, M.B. 2009. How to make evolution-proof insecticides for malaria control. PLoS Biology 7: e1000058.

Insecticides are one of the cheapest, most effective, and best proven methods of controlling malaria, but mosquitoes can rapidly evolve resistance. Such evolution, first seen in the 1950s in areas of widespread DDT use, is a major challenge because attempts to comprehensively control and even eliminate malaria rely heavily on indoor house spraying and insecticide-treated bed nets. Current strategies for dealing with resistance evolution are expensive and open ended, and their sustainability has yet to be demonstrated. Here we show that if insecticides targeted old mosquitoes, and ideally old malaria-infected mosquitoes, they could provide effective malaria control while only weakly selecting for resistance. This alone would greatly enhance the useful life span of an insecticide. However, such weak selection for resistance can easily be overwhelmed if resistance is associated with fitness costs. In that case, late-life–acting insecticides would never be undermined by mosquito evolution. We discuss a number of practical ways to achieve this, including different use of existing chemical insecticides, biopesticides, and novel chemistry. Done right, a one-off investment in a single insecticide would solve the problem of mosquito resistance forever.

Abigail Lustig testimony in Texas.

I feel very strongly that scientists should know the history of their discipline, as this is of substantial importance in guiding new research and preventing the same tired arguments from continually resurfacing (case in point, the myth that “junk DNA” was dismissed as totally nonfunctional or that epigenetics represents “neo-Lamarckism”). In this sense, the lessons provided by historians and philosophers can be relevant for modern science. Familiarity with the history of science is also critical for effective teaching, so again, historians can play an influential role in improving science education. This is true not only for university-level science courses taught by professional scientists, but also in protecting education standards at the high school level.

Here is an example of that — Dr. Abigail Lustig, a historian at the University of Texas Austin, presenting her testimony before the Texas Board of Education. It is very brief, but eloquently clarifies the crucial distinction between evolution as fact and as theory, and the substantial difference in historical debate and timing of acceptance of Darwin’s ideas on these two issues.

For my take, see Evolution as fact, theory, and path in E:EO.

Danish, anybody?

Sadly, I can’t read Danish and therefore I am not sure quite what this article in Ingeniøren actually says.

Evolutionsteorien er under stadig udvikling

However, I can say that the author, Robin Engelhardt, was not only pleasant but he absolutely had done his homework and grasped the issue (whether the rise of epigenetics constitutes neo-Lamarckism) quite well. I wish more science writers would take this example!

Walking seal.

Other bloggers and authors have already covered the discovery of Puijila darwini by Rybczynski et al (2009), a transitional fossil (but not a lineal ancestor) between modern pinnipeds (seals and kin) and terrestrial mammals. See, e.g., Not Exactly Rocket Science, Origins, Laelaps, ScienceNOW, Discovery Channel, ScienceNews, Scientific American, and so on…

For lots of information, see the resources provided by the Canadian Museum of Nature.


Like Tiktaalik, this species was discovered in the Canadian Arctic and bears an Inuktitut name.

Etymology. Puijila (Inuktitut): young sea mammal, often referring to a seal; darwini: for Charles Darwin, who wrote with his usual prescience, “A strictly terrestrial animal, by occasionally hunting for food in shallow water, then in streams or lakes, might at last be converted into an animal so thoroughly aquatic as to brave the open ocean”.


Here’s something the other bloggers probably cannot say, though: I have been to Devon Island where it was located!

Understanding natural selection.

My most recent paper in Evolution: Education and Outreach, which is part of a series on natural selection, is available in preprint form.

Understanding natural selection: essential concepts and common misconceptions
T. Ryan Gregory

Natural selection is one of the central mechanisms of evolutionary change and is the process responsible for the evolution of adaptive features. Without a working knowledge of natural selection, it is impossible to understand how or why living things have come to exhibit their diversity and complexity. An understanding of natural selection also is becoming increasingly relevant in practical contexts, including medicine, agriculture, and resource management. Unfortunately, studies indicate that natural selection is generally very poorly understood, even among many individuals with postsecondary biological education. This paper provides an overview of the basic process of natural selection, discusses the extent and possible causes of misunderstandings of the process, and presents a review of the most common misconceptions that must be corrected before a functional understanding of natural selection and adaptive evolution can be achieved.

Click here to download.

"Evolution-proof"?

A while ago I posted about some claims that a snake species had evolved an “unbeatable” predation tactic.

Orgel’s Second Rule and “unbeatable” predation tactics

I also posted about a claim that an antibiotic had been invented to which bacteria could not evolve resistance.

“Everlasting antibiotics”, wanna bet?

Here is the most recent in this series of “I can’t imagine how evolution could occur in this circumstance” silliness.

How to Make Evolution-Proof Insecticides for Malaria Control

Insecticides are one of the cheapest, most effective, and best proven methods of controlling malaria, but mosquitoes can rapidly evolve resistance. Such evolution, first seen in the 1950s in areas of widespread DDT use, is a major challenge because attempts to comprehensively control and even eliminate malaria rely heavily on indoor house spraying and insecticide-treated bed nets. Current strategies for dealing with resistance evolution are expensive and open ended, and their sustainability has yet to be demonstrated. Here we show that if insecticides targeted old mosquitoes, and ideally old malaria-infected mosquitoes, they could provide effective malaria control while only weakly selecting for resistance. This alone would greatly enhance the useful life span of an insecticide. However, such weak selection for resistance can easily be overwhelmed if resistance is associated with fitness costs. In that case, late-life–acting insecticides would never be undermined by mosquito evolution. We discuss a number of practical ways to achieve this, including different use of existing chemical insecticides, biopesticides, and novel chemistry. Done right, a one-off investment in a single insecticide would solve the problem of mosquito resistance forever.

Ok readers, go see their paper, then post ideas regarding how evolution might still occur either in the mosquitoes or Plasmodium to make this not so very “evolution-proof” after all.

Hint: Note the following specifics:

The population genetics model makes the following assumptions:

1. Adult mosquito population size is constant.
2. Mosquitoes do not complete more than ten gonotrophic cycles.
3. The genetic make-up of mating males in any cycle is the same as that calculated for newly hatched mosquitoes in that cycle.
4. Males of all resistant/susceptibility genotypes are equally likely to mate successfully.
5. Females mate once only, in their first cycle, as is the norm.
6. Number of eggs produced per laying female is unaffected by egg paternal genotype.
7. Genotypes of emerging adults joining the population are in the same proportions as the genotypes of the generation of eggs from which they hatch.
8. Resistance is dominant, as can be the case.
9. Costs of resistance are dominant.
10. The proportion of infectious humans is constant.

The feeding cycle model makes the following assumptions.

1. Mosquitoes bite humans randomly and uniformly.
2. Malaria-infected mosquitoes never become uninfected.
3. The proportion of humans who are infectious is constant.
4. A variety of parameters do not change over successive gonotrophic cycles: (i) the background mosquito mortality rate (what Smith and McKenzie call “force of mortality”), which is considered as a constant per-capita daily death rate (i.e. there is no senescence), (ii) the probability of taking a blood meal and (iii) the probability of feeding on a human.
5. Conventional insecticides are instant kill.

I’ll point out again what Orgel’s second rule says: Evolution is cleverer than you are.